Fixed some small errors.

FRC_heinz.sh

@@ -16,7 +16,7 @@ do
 done
 DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
 # Use a single file for logging, use the starttime as identifier
-LOGFILE="kmerfreq_heinz."`date +%Y%m%d_%k%M%S`.out
+LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
 
 # Input assembly
 #allpaths       /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
@@ -27,12 +27,12 @@ LOGFILE="kmerfreq_heinz."`date +%Y%m%d_%k%M%S`.out
 
 ASSEMBLY=/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
 PREFIX=allpaths_lg
-$MIN_PE_INS=320
-$MAX_PE_INS=430
-$MIN_MP_INS=2435
-$MAX_MP_INS=3555
-$ESTIMATED_GENOME_SIZE=760000000
-$OUTPUT_HEADER=${PREFIX}.FRC.
+MIN_PE_INS=320
+MAX_PE_INS=430
+MIN_MP_INS=2435
+MAX_MP_INS=3555
+ESTIMATED_GENOME_SIZE=760000000
+OUTPUT_HEADER=${PREFIX}.FRC.
 
 # Map reads against assembly with BWA
 # Create index
@@ -68,7 +68,10 @@ fi
 	# Create SAM files of the paired mappings
 	for name in rc_3018DAAXX_2 rc_30THBAAXX_2
 	do
-		bwa sampe -P ${PREFIX} ${PREFIX}.${name}_f.sai ${PREFIX}.${name}_r.sai ${name}_f.fastq ${name}_r.fastq > ${PREFIX}.${name}.sam
+		bwa sampe -P ${PREFIX} \
+		${PREFIX}.${name}_f.sai ${PREFIX}.${name}_r.sai \
+		${name}_f.fastq ${name}_r.fastq \
+		> ${PREFIX}.${name}.sam
 		# Convert result to BAM
 		samtools view -S ${PREFIX}.${name}.sam -b > ${PREFIX}.${name}.bam
 		# Sort the BAM
@@ -78,7 +81,8 @@ fi
 	done
 	# Merge the created BAMs
 	samtools merge -r -1 ${PREFIX}.MP.bam ${PREFIX}.rc_3018DAAXX_2.sorted.bam ${PREFIX}.rc_30THBAAXX_2.sorted.bam
-# The PE data : /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/*.64.fastq
+
+# PE data
 	# Map PE reads
 	for file in /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R1_001.64.fastq /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R2_001.64.fastq
 	do
@@ -97,8 +101,8 @@ fi
 	samtools sort ${PREFIX}.PE.bam ${PREFIX}.PE.sorted
 	# Index the BAM
 	samtools index ${PREFIX}.PE.sorted.bam
-# run FRC
 
+# run FRC as per README
 FRC 	--pe-sam ${PREFIX}.PE.sorted.ba \
 	--pe-min-insert $MIN_PE_INS \
 	--pe-max-insert $MAX_PE_INS \
@@ -108,5 +112,7 @@ FRC 	--pe-sam ${PREFIX}.PE.sorted.ba \
 	--genome-size $ESTIMATED_GENOME_SIZE \
 	--output $OUTPUT_HEADER \
 
+# TODO : Create better CE statisitcs
+